Sam travels through time via Celebi in Celebi: Voice of the Forest. There, he encounters Ash and his friends. It is unknown if the events in the future and return to the past directly alter the original timeline, but it is hinted that it might not have and these events were already present in the original timeline.

Ritchie travels through time via Celebi in Celebi and Joy. Events in the past directly alter the original timeline.

Calista travels through time via Baltoy and an alter in Me, Myself and Time. It's also a case of meeting one's younger self. It is unknown if the events in the past directly alter the original timeline.

Ferris travels through time via a portal in A Restoration Confrontation!. It is also a case of arriving in the far distant past as opposed to the recent past. It is unknown if the events in the past directly alter the original timeline.

In the manga

In the Pokémon Adventures manga

The Masked Man desires Celebi's time-traveling ability to reunite himself with his two lost Pokémon. He wound up disappearing into Celebi's time vortex.